WIP
scpGUI is a shiny application that serves as a graphical
interface for the scp
package (Vanderaa and Gatto (2021)).
It leverages the power of Shiny and ShinydashboardPlus to provide a
user-friendly interface for SCP data analysis. The app is organized into
multiple sections, each dedicated to a specific aspect of SCP data
processing. These sections are documented in separate vignettes to make
it easy for users to navigate and find information relevant to their
needs.
scp Package
scpGUI is a graphical interface for the scp
package it is therefore recommended to understand how
scp will handle the SCP data. In this short section, the
general idea behind scp is presented refer to the documentation
of the package for more information.
The scp
package is a robust tool for processing and analyzing MS-based SCP
data. It operates on a specialized data structure that wraps QFeatures
objects (Gatto (2020)) around SingleCellExperiment
objects (Amezquita et al. (2020)). This
unique data structure can be conceptualized as Matryoshka dolls, where
SingleCellExperiment objects are the small dolls contained within the
larger QFeatures doll.
The SingleCellExperiment
class provides a dedicated framework for single-cell data, acting as an
interface to cutting-edge methods for processing, visualizing, and
analyzing single-cell data. The QFeatures
class, on the other hand, is a data framework specifically designed to
manipulate and process MS-based quantitative data. It preserves the
relationship between different levels of information, such as peptide to
spectrum match (PSM) data, peptide data, and protein data. Additionally,
the QFeatures package offers an interface to various utility functions
that streamline the processing of MS data. For further details on MS
data analysis tools, refer to the RforMassSpectrometry
project.
Before diving into the SCP data analysis using scpGUI,
it’s essential to note that this app serves as an interface to the
scp package. When errors occur during the analysis,
scpGUI will report the error message in a dropdown menu at
the top right of the screen. In such cases, users are encouraged to
refer to the documentation of the associated function within the
scp package to identify and resolve the issue. The error
messages provide valuable clues, and searching the scp
package documentation will help users troubleshoot effectively.
# Check if remotes is installed. Otherwise install it.
if (!require("remotes", quietly = TRUE)) {
install.packages("remotes")
}
# Install the package
#remotes::install_github("UCLouvain-CBIO/scpGUI")
# Load the package
#library(scpGUI)
app <- scpGUI(example = FALSE)
if (interactive()) {
shiny::runApp(app)
}When launching scpGUI, the user can see section of the
app on the right sidebar. Each section will serve one step of the
workflow. Each section is documented in its own vignette: